Great progress has been made in sleep medical research in recent years and sleep medicine has thus evolved into a specialized medical field. Sleep apnea syndrome is one of the mostly commonly seen sleep disorders. It is now clear that sleep apnea has adverse effects on the heart and is a risk factor for several cardiovascular diseases. Studies have found that decreased heart rate variability (HRV) is a prognostic factor for cardiovascular disease and it also associated with higher mortality rate. Considering the confounding effect of BMI and sleep apnea severity, this work investigates the correlation between heart rate variability and AHI (apnea-hypopnea index which is used to characterize the severity of sleep apnea) by dividing patients into different BMI subgroups. This work includes 1068 male subjects with complete overnight ECG recordings. The low-frequency (LF), the high-frequency (HF) component and the LF/HF ratio of HRV are computed for the 10 BMI subgroups. The Bootstrap method and the BCa technique for confidence interval estimation are employed to verify the linear association between the HRV measures and the severity of sleep apnea. The experimental results show that statically significant correlation exist between LF/HF ratio and AHI for BMI ¡Ù28 patient groups. Statically significant correlation between LF and AHI also exists for BMI ¡Ù27 patient groups. These results demonstrate that the associations between some of the HRV measures and AHI are clearly BMI dependent.